Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398499.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1794.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10579
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.20
Warning! 4715 characters in sequence are not A, C, G, or T
Found at i:6153 original size:172 final size:171
Alignment explanation
Indices: 5503--6161 Score: 494
Period size: 172 Copynumber: 3.8 Consensus size: 171
5493 NNNNNNNAAC
* ** *
5503 GGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACTTTTTTTGCTAAAATAGACTAT
1 GGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAAAACAGACTAT
* *** * * * * **********
5568 AATTGATTTTTTACCTTGGGAAACATGTAGAAAAAGCCATTCATTAAGAAGAAAANNNNNNNNNN
66 AATTGAATACCTGCCTTAGAAAACATGCAGAAAAAGCCATTCATTAAGAAGAAAAGTCCATTTAT
* * *
5633 AGTCACTCATTCCTTTAAAAGCCTTATTACCCACTTTGAAG
131 AGTCACTCATTCCTTCAAAAGCCTTATTACCCACTTTAAAA
* * * *
5674 GGTTTTATAATCTCATAATTGATTTTAAGTTGAAATTTTTTGCATTTTTTGTTAAAAGAGACTAT
1 GGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAAAACAGACTAT
* ** * *
5739 AATTGAATACCTGCCTTAGGAAATGTACAGAAAAAGCCTGTTCATTAAGAAGAAAAGTCCATTTA
66 AATTGAATACCTGCCTTAGAAAACATGCAGAAAAAGCC-ATTCATTAAGAAGAAAAGTCCATTTA
* * * * * * *
5804 TAGTAACCCACTCCTTCTAAAGGCTTATTACTCTCTTTAAAA
130 TAGTCACTCATTCCTTCAAAAGCCTTATTACCCACTTTAAAA
* ********** * * *
5846 AGTTTTATAATCTCNNNNNNNNNNTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGATTCT
1 GGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAAAACAGACTAT
* * ** * * * * **********
5911 AAGTGATTGTCTGCCTTGGAAAACGA-GTAGAAAAAGTCATTCATTGAGAAGAAANNNNNNNNNN
66 AATTGAATACCTGCCTTAGAAAAC-ATGCAGAAAAAGCCATTCATTAAGAAGAAAAGTCCATTTA
* ** * * *
5975 TAGTCACTCATTTCTTCAAAAGCCTTAAAACCCGCTTTTAAT
130 TAGTCACTCATTCCTTCAAAAGCCTTATTACCCACTTTAAAA
* * *
6017 GGTTTTATACTCTCATAATTAATTTTAAGTTGAATTTTTTTATATTTTTTTATTAAAACAGACTA
1 GGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTTATTAAAACAGACTA
* * * *
6082 TAATTAAATACCTGCCTTAAAAAACATGCAAAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTA
65 TAATTGAATACCTGCCTTAGAAAACATGCAGAAAAAGCCATTCATTAAGAAGAAAAGTCCATTTA
6147 TAGTCAC-CTATTCCT
130 TAGTCACTC-ATTCCT
6162 NNNNNNNNNN
Statistics
Matches: 357, Mismatches: 126, Indels: 9
0.73 0.26 0.02
Matches are distributed among these distances:
171 165 0.46
172 192 0.54
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.36
Consensus pattern (171 bp):
GGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAAAACAGACTAT
AATTGAATACCTGCCTTAGAAAACATGCAGAAAAAGCCATTCATTAAGAAGAAAAGTCCATTTAT
AGTCACTCATTCCTTCAAAAGCCTTATTACCCACTTTAAAA
Found at i:8729 original size:171 final size:170
Alignment explanation
Indices: 8396--8974 Score: 727
Period size: 171 Copynumber: 3.4 Consensus size: 170
8386 GAAAATGTAA
*
8396 AAAATTAATTATGAGATTATAAAACCATTTAAACCGAGTAATAAGGCTTTTGACA-GAAT-AGGT
1 AAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA-GCTTTTGA-AGGAATGA-GT
* * *
8459 GACTATAAATGGACTTTTCTTCTCAATGAATGG-TTTTTTTGCACGTTTTTTAAGGTAGGTATTT
63 GACTATAAATGGACTTTTCTTCTCAATGAATGGATTTTTTTGCACGTTTTCTAAGGCAGGCATTT
* * *
8523 AATTATAGTCTGTTTGAATAAAAAAATGCAAAAAAATTCAACTT
128 AATTATAGTCTGTTTTAA-CAAAAAATGTAAAAAAATTCAACTT
* * * *
8567 AAAATGAATTATGAGATTTTAAAACCATTTAAAGCGAGAAATAACGCTTTTGAAGGAATGAGTAA
1 AAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA-GCTTTTGAAGGAATGAGTGA
* * * * * * ** * * *
8632 CTATAAATAGACTTTTTTTCTCAATGAATGGATTTTTCTACATGTTTTCCAAGGCAAACAATCAC
65 CTATAAATGGACTTTTCTTCTCAATGAATGGATTTTTTTGCACGTTTTCTAAGGCAGGCATTTAA
* *
8697 TGATAGTCTGTTTTAACAGAAAATGTAAAAAAATTCAACTT
130 TTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTT
* ** *
8738 AAAATCAATTACAAGATTATAAAACCGTTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGA
1 AAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG-CTTTTGAAGGAATGAGTGA
* * *
8803 CTAGAAATGGAGTTTTCTTCTCAATGAAT-GATTTTTTTGCACG-TTTCTTGAGGCAGGCATTTA
65 CTATAAATGGACTTTTCTTCTCAATGAATGGATTTTTTTGCACGTTTTC-TAAGGCAGGCATTTA
*
8866 ATTATAGTCTGTTTTAACAAAAAATCTAAAAAAATTCAACTT
129 ATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTT
* * * *
8908 AAAATTAATTTTGAAATTATAAAACCGTTTAAAGTGAGTAATAAGCTTTTTGAAGGAATGAGTGA
1 AAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGC-TTTTGAAGGAATGAGTGA
8973 CT
65 CT
8975 CTNNNNNNNN
Statistics
Matches: 347, Mismatches: 55, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
169 5 0.01
170 119 0.34
171 187 0.54
172 36 0.10
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (170 bp):
AAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCTTTTGAAGGAATGAGTGAC
TATAAATGGACTTTTCTTCTCAATGAATGGATTTTTTTGCACGTTTTCTAAGGCAGGCATTTAAT
TATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTT
Done.